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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Step 15 error: Error in unlist(object) : long vectors not supported yet: #379

Closed adhisadi closed 2 years ago

adhisadi commented 2 years ago

Hi, I am running infercnv_1.10.1 on 10X dataset in over 80k cells. infercnv_run = infercnv::run(infercnv_obj = infercnv_obj, cutoff=0.1, out_dir="nov_22_output_files", analysis_mode="subclusters", cluster_by_groups=F, plot_steps=F, denoise=T, no_prelim_plot=F, HMM=T)

I am running through this error in step15: STEP 15: computing tumor subclusters via leiden

INFO [2021-11-23 11:00:46] define_signif_tumor_subclusters(p_val=0.1 INFO [2021-11-23 11:00:46] define_signif_tumor_subclusters(), tumor: all_observations Error in unlist(object) : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:537 Calls: ... .single_tumor_leiden_subclustering -> leiden -> leiden.matrix -> unlist Execution halted

Could you provide some instruction on how to solve this issue? Thank you.

GeorgescuC commented 2 years ago

Hi @adhisadi ,

This issue should be fixed in the latest devel version 1.11.1 that you can find on BioConductor, or the master branch on GitHub.

Regards, Christophe.